diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 76c9bf65..06c22a58 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -8,6 +8,7 @@ on: - pull_request jobs: + build: runs-on: ${{ matrix.os }} diff --git a/.github/workflows/convert_csv.yml b/.github/workflows/convert_csv.yml new file mode 100644 index 00000000..844a2e50 --- /dev/null +++ b/.github/workflows/convert_csv.yml @@ -0,0 +1,37 @@ +# This workflow will install Python dependencies, run tests and lint with a variety of Python versions +# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions + +name: convert_csv + +on: + - push + +jobs: + + convert_csv_to_md: + runs-on: ${{ matrix.os }} + strategy: + matrix: + os: [ubuntu-latest] + python-version: [3.8] + + steps: + - uses: actions/checkout@v2 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v1 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + pip install wheel pandas + pip install wheel tabulate + - name: Run script to convert table + run: | + python doc/convert_to_md.py + - name: Commit md file + run: | + git add doc/code_contributions_record.md + git config --global user.name 'OSIPI' + git config --global user.email 'OSIPI@users.noreply.github.com' + git diff --exit-code || git commit -am "commit code_contributions_record.md" + git push diff --git a/README.md b/README.md index ed7cf1ed..9b44cba6 100644 --- a/README.md +++ b/README.md @@ -3,6 +3,11 @@ [![build Actions Status](https://github.com/OSIPI/DCE-DSC-MRI_CodeCollection/workflows/ci/badge.svg)](https://github.com/OSIPI/DCE-DSC-MRI_CodeCollection/actions) [![codecov](https://codecov.io/gh/OSIPI/DCE-DSC-MRI_CodeCollection/branch/develop/graph/badge.svg?token=ZR3RPV8Y0B)](https://codecov.io/gh/OSIPI/DCE-DSC-MRI_CodeCollection) + + +- [code database with links to source code](doc/code_contributions_record.md) +- [test-results website](http://osipi.org/DCE-DSC-MRI_TestResults) + The ISMRM Open Science Initiative for Perfusion Imaging ([OSIPI](https://www.osipi.org/)) aims to promote the sharing of perfusion imaging software in order to reduce duplication, improve reproducibility and speed up translation. This **DCE-DSC-MRI_CodeCollection** code library is maintained by [Taskforce 2.3](https://www.osipi.org/task-force-2-3/) of OSIPI and aims to collect, test and share open-source perfusion imaging code for use in research and software development. Code contributions can include modules covering one or more steps within the image processing pipeline, for example T1 mapping, converting signal to concentration and pharmacokinetic modelling. A further aim of OSIPI is to develop a fully tested and harmonised code library, drawing on the contributions within this repository. A summary of the repository structure is shown below. More detailed information and documentation is located in the repository [wiki](https://github.com/OSIPI/DCE-DSC-MRI_CodeCollection/wiki) @@ -10,7 +15,7 @@ A summary of the repository structure is shown below. More detailed information ``` OSIPI/DCE-DSC-MRI_CodeCollection ├── doc -│ └── code_contributions_record.csv # Overview of code contributions +│ └── code_contributions_record.md # Overview of code contributions ├── src │ └── original # Original contributed code organized per contribution │ └── DS_BW_VanderBiltUMC_USA @@ -31,7 +36,8 @@ OSIPI/DCE-DSC-MRI_CodeCollection Wiki # Information and guidelines ``` -Click [here](https://github.com/OSIPI/DCE-DSC-MRI_CodeCollection/blob/develop/doc/code_contributions_record.csv) for database of code available and testing status +Click [here](doc/code_contributions_record.md) for +database of code available with links to code. The results of the validated code are published on the [test-results website](http://osipi.org/DCE-DSC-MRI_TestResults), which is hosted via a separate [repository](https://github.com/OSIPI/DCE-DSC-MRI_TestResults). diff --git a/doc/code_contributions_record.csv b/doc/code_contributions_record.csv index 104c0e96..821978e4 100644 --- a/doc/code_contributions_record.csv +++ b/doc/code_contributions_record.csv @@ -1,88 +1,88 @@ -Technique,Category,Subcategory,Notes,Subfolder,Authors,Institution,function/module name,doi,Tester,Test status (empty/in-progress/complete) -DCE,Bolus arrival time,piecewise linear quadratic function,Cheong et al (DOI: 10.1088/0031-9155/48/5/403),LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",BAT_linquad,,tbd, -DCE,Bolus arrival time,fitting Kety (Tofts) model to first third of the curve,,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",BAT_kety,,tbd, -DCE,Input Functions,load AIF,load from txt,MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",read_AIF,https://doi.org/10.21105/joss.03523,tbd, -DCE,Input Functions,Parker AIF,,MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",compute_population_AIF,https://doi.org/10.21105/joss.03523,JK/PvH,completed -DCE,Input Functions,patient-specific AIF,constructed from time-concentration data,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",patientSpecific,,tbd, -DCE,Input Functions,Parker AIF,"Parker AIF, Parker-like AIF",MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",Parker,,JK/PvH,completed -DCE,Input Functions,Manning AIF,Manning et al (https://doi.org/10.1002/mrm.28833),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","ManningFast, ManningSlow",,tbd,completed -DCE,Input Functions,Heye AIF,Heye et al (https://doi.org/10.1016/j.neuroimage.2015.10.018),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",Heye,,tbd,completed -DCE,Input Functions,AIF parameterization,,OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK","Cosine4AIF, Cosine8AIF",https://doi.org/10.1088/0031-9155/53/5/005; https://doi.org/10.1007/s00330-015-4012-9,tbd, -DCE,Input Functions,Head-and-neck population AIF,Wong et al (DOI: https://doi.org/10.2967/jnumed.116.174433),OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",aifPopHN,,tbd, -DCE,Input Functions,Parker AIF,,OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",aifPopPMB,,tbd, -DCE,Input Functions,load AIF,from txt,OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway",loadStandard,,tbd, -DCE,Input Functions,AIF parameterization,fit gamma-variate function,OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway",gammaVariateFit,,tbd, -DCE,Input Functions,Georgiou AIF,Georgiou et al (DOI: 10.1002/mrm.27524),PvH_NKI,Petra van Houdt,"the Netherlands Cancer Institute, the Netherlands",GeorgiouAIF,,JK/PvH,completed -DCE,Input Functions,Parker AIF,,PvH_NKI,Petra van Houdt,"the Netherlands Cancer Institute, the Netherlands",ParkerAIF,,JK/PvH,completed -DCE,Input Functions,Parker AIF,,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia","AIF, variableAIF",,JK/PvH,completed -DCE,Input Functions,preclinical AIF,McGrath et al (DOI: 10.1002/mrm.21959),ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",preclinicalAIF,,JK/PvH,completed -DCE,Miscellaneous,enhancement detection,check for enhancement,OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",enhance,,tbd, -DCE,Parameter derivation,iAUC,,MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",compute_IAUC,https://doi.org/10.21105/joss.03523,tbd, -DCE,Pharmacokinetic models,Tofts,NLLS fitting (+forward model),DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA","tofts_integral, fit_tofts_model",,tdd, -DCE,Pharmacokinetic models,extended Tofts,NLLS fitting (+forward model),DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA","ext_tofts_integral, fit_tofts_model",,tbd, -DCE,Pharmacokinetic models,Tofts,NLLS fitting (+ forward model),LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA","tofts_model, fit_tofts",,ST/OGC,completed -DCE,Pharmacokinetic models,2-cmp exchange,forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",TwoCXM,,MJT,completed -DCE,Pharmacokinetic models,2-cmp uptake,forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",TwoCUM,,MJT,completed -DCE,Pharmacokinetic models,AATH,forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",AATH,,tbd, -DCE,Pharmacokinetic models,extended Tofts,forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",ExtKety,,ST/OGC,completed -DCE,Pharmacokinetic models,Patlak,forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",Patlak,,MJT,completed -DCE,Pharmacokinetic models,Tofts,forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",Kety,,ST/OGC,completed -DCE,Pharmacokinetic models,2-cmp exchange,LLSQ fitting (+forward model),MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",two_cxm_model,https://doi.org/10.21105/joss.03523,MJT,completed -DCE,Pharmacokinetic models,2-cmp filtration,LLSQ fitting (+forward model),MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",two_cfm_model,https://doi.org/10.21105/joss.03523,tbd, -DCE,Pharmacokinetic models,active uptake and efflux (AUEM),LLSQ fitting (+forward model),MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",active_uptake_model,https://doi.org/10.21105/joss.03523,tbd, -DCE,Pharmacokinetic models,dual-inlet general model,LLSQ fitting (+forward model),MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",dibem,https://doi.org/10.21105/joss.03523,tbd, -DCE,Pharmacokinetic models,extended Tofts,LLSQ fitting (+forward model),MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",tofts_model,https://doi.org/10.21105/joss.03523,ST/OGC,completed -DCE,Pharmacokinetic models,2-cmp exchange,NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","TCXM, EnhToPKP, ConcToPKP",,MJT,completed -DCE,Pharmacokinetic models,2-cmp exchange,NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","TCXM, EnhToPKP, ConcToPKP",,MJT,completed -DCE,Pharmacokinetic models,2-cmp uptake,NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","TCUM, EnhToPKP, ConcToPKP",,MJT,completed -DCE,Pharmacokinetic models,2-cmp uptake,NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","TCUM, EnhToPKP, ConcToPKP",,MJT,completed -DCE,Pharmacokinetic models,extended Tofts,NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","ExtendedTofts, EnhToPKP, ConcToPKP",,ST/OGC,completed -DCE,Pharmacokinetic models,extended Tofts,NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","ExtendedTofts, EnhToPKP, ConcToPKP",,ST/OGC,completed -DCE,Pharmacokinetic models,Patlak,NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","Patlak, EnhToPKP, ConcToPKP",,MJT,completed -DCE,Pharmacokinetic models,Patlak,NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","Patlak, EnhToPKP, ConcToPKP",,MJT,completed -DCE,Pharmacokinetic models,Patlak,LLSQ fitting,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",PatlakLinear,,MJT,completed -DCE,Pharmacokinetic models,steady-state vp,NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","SteadyStateVp, EnhToPKP, ConcToPKP",,tbd, -DCE,Pharmacokinetic models,steady-state vp,NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","SteadyStateVp, EnhToPKP, ConcToPKP",,tbd, -DCE,Pharmacokinetic models,Tofts,NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","Tofts, EnhToPKP, ConcToPKP",,ST/OGC,completed -DCE,Pharmacokinetic models,Tofts,NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","Tofts,EnhToPKP, ConcToPKP",,ST/OGC,completed -DCE,Pharmacokinetic models,extended Tofts,NLLS fitting (+forward model),OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",fit_tofts_model,,ST/OGC,completed -DCE,Pharmacokinetic models,2-cmp exchange,LLSQ fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway","twoCXM, fitToModelLLSQ",,MJT,completed -DCE,Pharmacokinetic models,extended Tofts,NLLS fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway","ETM, fitToModelNLLS, fitToModelNLLS_parallel",,ST/OGC,completed -DCE,Pharmacokinetic models,extended Tofts,LLSQ fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway","ETM, fitToModelLLSQ",,ST/OGC,completed -DCE,Pharmacokinetic models,Tofts,NLLS fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway","TM, fitToModelNLLS, fitToModelNLLS_parallel",,ST/OGC,completed -DCE,Pharmacokinetic models,Tofts,LLSQ fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, NOR","TM, fitToModelLLSQ",,ST/OGC,completed -DCE,Pharmacokinetic models,1-cmp,forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",OneCompartment,,tbd, -DCE,Pharmacokinetic models,dual-inlet 1-cmp,forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",DualInletOneCompartment,,tbd, -DCE,Pharmacokinetic models,dual-inlet ext Tofts,forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",DualInletExtendedTofts,,tbd, -DCE,Pharmacokinetic models,dual-inlet high-flow 2-cmp Gadoxetate,forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",DualInletconc_HF2CGM,,tbd, -DCE,Pharmacokinetic models,extended Tofts,forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",ExtendedTofts,,ST/OGC,completed -DCE,Pharmacokinetic models,Tofts,forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",Tofts,,ST/OGC,completed -DCE,Pharmacokinetic models,high flow 2-cmp Gadoxetate,forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",,,tbd, -DCE,Pharmacokinetic models,Patlak,forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",PatlakModel,,MJT,completed -DCE,Signal to Concentration,SPGR,"two-steps: S->R1, R1->C",DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA","r1eff_to_conc, dce_to_r1eff",,tbd, -DCE,Signal to Concentration,SPGR or GE-EPI,,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA","signal_to_conc, estimate_delta_R1",,LK,completed -DCE,Signal to concentration,SPGR,"reverse C->S also available",LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",SI2Conc,,LK,completed -DCE,Signal to concentration,SPGR,"reverse C->S also available",MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",signal_to_concentration,https://doi.org/10.21105/joss.03523,LK,completed -DCE,Signal to concentration,SPGR,"two steps: S-> enhancement, enhancement -> C; reverse C->S also available",MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","sign_to_enh, enh_to_conc",,LK,completed -DCE,Signal to concentration,SPGR,"two steps: S->R1, R1 -> C; reverse C->S also available",OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK","dce_to_r1eff, r1eff_to_conc",,LK,completed -DCE,Signal to concentration,SPGR,"reverse R1->C also available",ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",signals2conc,,LK,completed -DCE,T1,VFA,nonlinear,DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA",fit_R1,,tbd, -DCE,T1,VFA,despot,McGill_VFA,Zaki Ahmed,"McGill University, Canada",despot,,MJT,completed -DCE,T1,VFA,novifast,McGill_VFA,Zaki Ahmed,"McGill University, Canada",novifast,,MJT,completed -DCE,T1,DESPOT1-HIFI,Fit any combination of (IR-)SPGR scans to estimate T1,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",HIFI,,MJT,in-progress -DCE,T1,VFA,linear,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",VFALinear,,MJT,complete -DCE,T1,VFA,nonlinear,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",VFANonlinear,,MJT,complete -DCE,T1,VFA,two flip angles,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",VFA2Points,,tbd, -DCE,T1,VFA,two flip angles (linear),OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",R1_two_fas,,MJT,competed -DCE,T1,VFA,nonlinear,OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",R1_VFA,,MJT,competed -DCE,T1,VFA,linear,ST_Sydney_AUS_T1,Sirisha Tadimalla,"University of Sydney, Australia",VFAT1mapping,,MJT,completed -DCE,T1,VFA,nonlinear,ST_Sydney_AUS_T1,Sirisha Tadimalla,"University of Sydney, Australia",VFAT1mapping,,MJT,completed -DCE/DSC,AIF deconvolution,,,SR_TBG_BNI_PhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",AIFdeconvolution,,JA,completed -DCE/DSC,Miscellaneous,calculate SNR,,DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA",signal_to_noise_ratio,,tbd, -DCE/DSC,Miscellaneous,calculate enhancement ratio,,DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA",signal_enhancement_ratio,,tbd, -DSC,Input Functions,automatic AIF selection,"fully automatic, semi-automatic",JBJA_GUSahlgrenskaSWE,"Jesper Browall, Jonathan Arvidsson","Sahlgrenska University Hospital and Gothenburg University, Gothenburg, Sweden",AIF_selection_automatic.py,DOI: 10.1002/mrm.20759,tbd, -DSC,Leakage correction,BSW,,SR_TBG_BNI_PhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",BSWleakagecorr,,SR,in-progress -DSC,Parameter derivation,"CBV,CBF,MTT",,SR_TBG_BNI_PhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",DSCparameters,,tbd, -DSC,Signal to deltaR2*,single echo,,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA",,estimate_delta_R2s,tbd, -DSC,Signal to deltaR2*,dual echo,,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA",,"estimate_delta_R2s, estimate_delta_R2s_dual_echo",tbd, -DSC,Signal to R2*,dual echo,,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA",,estimate_R2s,tbd, \ No newline at end of file +Technique,Category,Subcategory (link to source code),Notes,Subfolder,Authors,Institution,function/module name,doi,Tester,Test status (empty/in-progress/complete) +DCE,Bolus arrival time,[piecewise linear quadratic function](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/BAT_estimation.py),Cheong et al (DOI: 10.1088/0031-9155/48/5/403),LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",BAT_linquad,,tbd, +DCE,Bolus arrival time,[fitting Kety (Tofts) model to first third of the curve](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/BAT_estimation.py),,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",BAT_kety,,tbd, +DCE,Input Functions,[load AIF](../src/original/MB_QBI_UoManchester_UK/QbiPy/dce_models/dce_aif.py),load from txt,MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",read_AIF,https://doi.org/10.21105/joss.03523,tbd, +DCE,Input Functions,[Parker AIF](../src/original/MB_QBI_UoManchester_UK/QbiPy/dce_models/dce_aif.py),,MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",compute_population_AIF,https://doi.org/10.21105/joss.03523,JK/PvH,completed +DCE,Input Functions,[patient-specific AIF](../src/original/MJT_UoEdinburgh_UK/aifs.py),constructed from time-concentration data,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",patientSpecific,,tbd, +DCE,Input Functions,[Parker AIF](../src/original/MJT_UoEdinburgh_UK/aifs.py),"Parker AIF, Parker-like AIF",MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",Parker,,JK/PvH,completed +DCE,Input Functions,[Manning AIF](../src/original/MJT_UoEdinburgh_UK/aifs.py),Manning et al (https://doi.org/10.1002/mrm.28833),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","ManningFast, ManningSlow",,tbd,completed +DCE,Input Functions,[Heye AIF](../src/original/MJT_UoEdinburgh_UK/aifs.py),Heye et al (https://doi.org/10.1016/j.neuroimage.2015.10.018),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",Heye,,tbd,completed +DCE,Input Functions,[AIF parameterization](../src/original/OG_MO_AUMC_ICR_RMH_NL_UK/ExtendedTofts/DCE.py),,OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK","Cosine4AIF, Cosine8AIF",https://doi.org/10.1088/0031-9155/53/5/005; https://doi.org/10.1007/s00330-015-4012-9,tbd, +DCE,Input Functions,[Head-and-neck population AIF](../src/original/OG_MO_AUMC_ICR_RMH_NL_UK/ExtendedTofts/DCE.py),Wong et al (DOI: https://doi.org/10.2967/jnumed.116.174433),OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",aifPopHN,,tbd, +DCE,Input Functions,[Parker AIF](../src/original/OG_MO_AUMC_ICR_RMH_NL_UK/ExtendedTofts/DCE.py),,OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",aifPopPMB,,tbd, +DCE,Input Functions,[load AIF](../src/original/OGJ_OsloU_NOR/MRImageAnalysis/DCE/ArterialInputFunction.py),from txt,OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway",loadStandard,,tbd, +DCE,Input Functions,[AIF parameterization](../src/original/OGJ_OsloU_NOR/MRImageAnalysis/DCE/ArterialInputFunction.py),fit gamma-variate function,OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway",gammaVariateFit,,tbd, +DCE,Input Functions,[Georgiou AIF](../src/original/PvH_NKI_NL/AIF/PopulationAIF.py),Georgiou et al (DOI: 10.1002/mrm.27524),PvH_NKI,Petra van Houdt,"the Netherlands Cancer Institute, the Netherlands",GeorgiouAIF,,JK/PvH,completed +DCE,Input Functions,[Parker AIF](../src/original/PvH_NKI_NL/AIF/PopulationAIF.py),,PvH_NKI,Petra van Houdt,"the Netherlands Cancer Institute, the Netherlands",ParkerAIF,,JK/PvH,completed +DCE,Input Functions,[Parker AIF](../src/original/ST_USyd_AUS/InputFunctions.py),,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia","AIF, variableAIF",,JK/PvH,completed +DCE,Input Functions,[preclinical AIF](../src/original/ST_USyd_AUS/InputFunctions.py),McGrath et al (DOI: 10.1002/mrm.21959),ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",preclinicalAIF,,JK/PvH,completed +DCE,Miscellaneous,[enhancement detection](../src/original/OG_MO_AUMC_ICR_RMH_NL_UK/ExtendedTofts/DCE.py),check for enhancement,OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",enhance,,tbd, +DCE,Parameter derivation,[iAUC](../src/original/MB_QBI_UoManchester_UK/QbiPy/dce_models/tissue_concentration.py),,MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",compute_IAUC,https://doi.org/10.21105/joss.03523,tbd, +DCE,Pharmacokinetic models,[Tofts](../src/original/DS_BW_VanderBiltUMC_USA/dcemri.py),NLLS fitting (+forward model),DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA","tofts_integral, fit_tofts_model",,tdd, +DCE,Pharmacokinetic models,[extended Tofts](../src/original/DS_BW_VanderBiltUMC_USA/dcemri.py),NLLS fitting (+forward model),DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA","ext_tofts_integral, fit_tofts_model",,tbd, +DCE,Pharmacokinetic models,[Tofts](../src/original/LCB_BNI_USA/dce.py),NLLS fitting (+ forward model),LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA","tofts_model, fit_tofts",,ST/OGC,completed +DCE,Pharmacokinetic models,[2-cmp exchange](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/models.py),forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",TwoCXM,,MJT,completed +DCE,Pharmacokinetic models,[2-cmp uptake](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/models.py),forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",TwoCUM,,MJT,completed +DCE,Pharmacokinetic models,[AATH](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/models.py),forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",AATH,,tbd, +DCE,Pharmacokinetic models,[extended Tofts](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/models.py),forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",ExtKety,,ST/OGC,completed +DCE,Pharmacokinetic models,[Patlak](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/models.py),forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",Patlak,,MJT,completed +DCE,Pharmacokinetic models,[Tofts](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/models.py),forward model,LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",Kety,,ST/OGC,completed +DCE,Pharmacokinetic models,[2-cmp exchange](../src/original/MB_QBI_UoManchester_UK/QbiPy/dce_models/two_cxm_model.py),LLSQ fitting (+forward model),MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",two_cxm_model,https://doi.org/10.21105/joss.03523,MJT,completed +DCE,Pharmacokinetic models,[2-cmp filtration](../src/original/MB_QBI_UoManchester_UK/QbiPy/dce_models/two_cfm_model.py),LLSQ fitting (+forward model),MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",two_cfm_model,https://doi.org/10.21105/joss.03523,tbd, +DCE,Pharmacokinetic models,[active uptake and efflux (AUEM)](../src/original/MB_QBI_UoManchester_UK/QbiPy/dce_models/active_uptake_model.py),LLSQ fitting (+forward model),MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",active_uptake_model,https://doi.org/10.21105/joss.03523,tbd, +DCE,Pharmacokinetic models,[dual-inlet general model](../src/original/MB_QBI_UoManchester_UK/QbiPy/dce_models/dibem.py),LLSQ fitting (+forward model),MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",dibem,https://doi.org/10.21105/joss.03523,tbd, +DCE,Pharmacokinetic models,[extended Tofts](../src/original/MB_QBI_UoManchester_UK/QbiPy/dce_models/tofts_model.py),LLSQ fitting (+forward model),MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",tofts_model,https://doi.org/10.21105/joss.03523,ST/OGC,completed +DCE,Pharmacokinetic models,[2-cmp exchange](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","TCXM, EnhToPKP, ConcToPKP",,MJT,completed +DCE,Pharmacokinetic models,[2-cmp exchange](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","TCXM, EnhToPKP, ConcToPKP",,MJT,completed +DCE,Pharmacokinetic models,[2-cmp uptake](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","TCUM, EnhToPKP, ConcToPKP",,MJT,completed +DCE,Pharmacokinetic models,[2-cmp uptake](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","TCUM, EnhToPKP, ConcToPKP",,MJT,completed +DCE,Pharmacokinetic models,[extended Tofts](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","ExtendedTofts, EnhToPKP, ConcToPKP",,ST/OGC,completed +DCE,Pharmacokinetic models,[extended Tofts](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","ExtendedTofts, EnhToPKP, ConcToPKP",,ST/OGC,completed +DCE,Pharmacokinetic models,[Patlak](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","Patlak, EnhToPKP, ConcToPKP",,MJT,completed +DCE,Pharmacokinetic models,[Patlak](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","Patlak, EnhToPKP, ConcToPKP",,MJT,completed +DCE,Pharmacokinetic models,[Patlak](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),LLSQ fitting,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",PatlakLinear,,MJT,completed +DCE,Pharmacokinetic models,[steady-state vp](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","SteadyStateVp, EnhToPKP, ConcToPKP",,tbd, +DCE,Pharmacokinetic models,[steady-state vp](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","SteadyStateVp, EnhToPKP, ConcToPKP",,tbd, +DCE,Pharmacokinetic models,[Tofts](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to concentration values (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","Tofts, EnhToPKP, ConcToPKP",,ST/OGC,completed +DCE,Pharmacokinetic models,[Tofts](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),NLLS fitting to signal incl. water exchange (incl forward model),MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","Tofts,EnhToPKP, ConcToPKP",,ST/OGC,completed +DCE,Pharmacokinetic models,[extended Tofts](../src/original/OG_MO_AUMC_ICR_RMH_NL_UK/ExtendedTofts/DCE.py),NLLS fitting (+forward model),OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",fit_tofts_model,,ST/OGC,completed +DCE,Pharmacokinetic models,[2-cmp exchange](../src/original/OGJ_OsloU_NOR/MRImageAnalysis/DCE/Analyze.py),LLSQ fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway","twoCXM, fitToModelLLSQ",,MJT,completed +DCE,Pharmacokinetic models,[extended Tofts](../src/original/OGJ_OsloU_NOR/MRImageAnalysis/DCE/Analyze.py),NLLS fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway","ETM, fitToModelNLLS, fitToModelNLLS_parallel",,ST/OGC,completed +DCE,Pharmacokinetic models,[extended Tofts](../src/original/OGJ_OsloU_NOR/MRImageAnalysis/DCE/Analyze.py),LLSQ fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway","ETM, fitToModelLLSQ",,ST/OGC,completed +DCE,Pharmacokinetic models,[Tofts](../src/original/OGJ_OsloU_NOR/MRImageAnalysis/DCE/Analyze.py),NLLS fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, Norway","TM, fitToModelNLLS, fitToModelNLLS_parallel",,ST/OGC,completed +DCE,Pharmacokinetic models,[Tofts](../src/original/OGJ_OsloU_NOR/MRImageAnalysis/DCE/Analyze.py),LLSQ fitting (+ forward model),OGJ_OsloU_NOR,Ole Gunnar Johansen,"University of Oslo, NOR","TM, fitToModelLLSQ",,ST/OGC,completed +DCE,Pharmacokinetic models,[1-cmp](../src/original/ST_USyd_AUS/ModelDictionary.py),forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",OneCompartment,,tbd, +DCE,Pharmacokinetic models,[dual-inlet 1-cmp](../src/original/ST_USyd_AUS/ModelDictionary.py),forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",DualInletOneCompartment,,tbd, +DCE,Pharmacokinetic models,[dual-inlet ext Tofts](../src/original/ST_USyd_AUS/ModelDictionary.py),forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",DualInletExtendedTofts,,tbd, +DCE,Pharmacokinetic models,[dual-inlet high-flow 2-cmp Gadoxetate](../src/original/ST_USyd_AUS/ModelDictionary.py),forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",DualInletconc_HF2CGM,,tbd, +DCE,Pharmacokinetic models,[extended Tofts](../src/original/ST_USyd_AUS/ModelDictionary.py),forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",ExtendedTofts,,ST/OGC,completed +DCE,Pharmacokinetic models,[Tofts](../src/original/ST_USyd_AUS/ModelDictionary.py),forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",Tofts,,ST/OGC,completed +DCE,Pharmacokinetic models,[high flow 2-cmp Gadoxetate](../src/original/ST_USyd_AUS/ModelDictionary.py),forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",,,tbd, +DCE,Pharmacokinetic models,[Patlak](../src/original/ST_USyd_AUS/ModelDictionary.py),forward model,ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",PatlakModel,,MJT,completed +DCE,Signal to Concentration,[SPGR](../src/original/DS_BW_VanderBiltUMC_USA/dcemri.py),"two-steps: S->R1, R1->C",DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA","r1eff_to_conc, dce_to_r1eff",,tbd, +DCE,Signal to Concentration,[SPGR or GE-EPI](../src/original/LCB_BNI_USA/dce.py),,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA","signal_to_conc, estimate_delta_R1",,LK,completed +DCE,Signal to concentration,[SPGR](../src/original/LEK_UoEdinburgh_UK/SignalToConcentration/SI2Conc.py),"reverse C->S also available",LEK_UoEdinburgh,Lucy Kershaw,"University of Edinburgh, UK",SI2Conc,,LK,completed +DCE,Signal to concentration,[SPGR](../src/original/MB_QBI_UoManchester_UK/QbiPy/dce_models/tissue_concentration.py),"reverse C->S also available",MB_QBI_UoManchester_UK,Michael Berks,"University of Manchester, UK",signal_to_concentration,https://doi.org/10.21105/joss.03523,LK,completed +DCE,Signal to concentration,[SPGR](../src/original/MJT_UoEdinburgh_UK/dce_fit.py),"two steps: S-> enhancement, enhancement -> C; reverse C->S also available",MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK","sign_to_enh, enh_to_conc",,LK,completed +DCE,Signal to concentration,[SPGR](../src/original/OG_MO_AUMC_ICR_RMH_NL_UK/ExtendedTofts/DCE.py),"two steps: S->R1, R1 -> C; reverse C->S also available",OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK","dce_to_r1eff, r1eff_to_conc",,LK,completed +DCE,Signal to concentration,[SPGR](../src/original/ST_USyd_AUS/signals2conc.py),"reverse R1->C also available",ST_USydAUS_DCE,Sirisha Tadimalla,"University of Sydney, Australia",signals2conc,,LK,completed +DCE,T1,[VFA](../src/original/DS_BW_VanderBiltUMC_USA/dcemri.py),nonlinear,DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA",fit_R1,,tbd, +DCE,T1,[VFA](../src/original/ZA_McGill_CAN/vfa.py),despot,McGill_VFA,Zaki Ahmed,"McGill University, Canada",despot,,MJT,completed +DCE,T1,[VFA](../src/original/ZA_McGill_CAN/vfa.py),novifast,McGill_VFA,Zaki Ahmed,"McGill University, Canada",novifast,,MJT,completed +DCE,T1,[DESPOT1-HIFI](../src/original/MJT_UoEdinburgh_UK/t1_fit.py),Fit any combination of (IR-)SPGR scans to estimate T1,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",HIFI,,MJT,in-progress +DCE,T1,[VFA](../src/original/MJT_UoEdinburgh_UK/t1_fit.py),linear,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",VFALinear,,MJT,complete +DCE,T1,[VFA](../src/original/MJT_UoEdinburgh_UK/t1_fit.py),nonlinear,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",VFANonlinear,,MJT,complete +DCE,T1,[VFA](../src/original/MJT_UoEdinburgh_UK/t1_fit.py),two flip angles,MJT_UoEdinburgh_UK,Michael Thrippleton,"University of Edinburgh, UK",VFA2Points,,tbd, +DCE,T1,[VFA](../src/original/OG_MO_AUMC_ICR_RMH_NL_UK/ExtendedTofts/DCE.py),two flip angles (linear),OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",R1_two_fas,,MJT,competed +DCE,T1,[VFA](../src/original/OG_MO_AUMC_ICR_RMH_NL_UK/ExtendedTofts/DCE.py),nonlinear,OG_MO_AUMC_ICR_RMH,"Oliver Gurney-Champion, Matthew Orton","Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK",R1_VFA,,MJT,competed +DCE,T1,[VFA](../src/original/ST_USyd_AUS/VFAT1mapping.py),linear,ST_Sydney_AUS_T1,Sirisha Tadimalla,"University of Sydney, Australia",VFAT1mapping,,MJT,completed +DCE,T1,[VFA](../src/original/ST_USyd_AUS/VFAT1mapping.py),nonlinear,ST_Sydney_AUS_T1,Sirisha Tadimalla,"University of Sydney, Australia",VFAT1mapping,,MJT,completed +DCE/DSC,AIF deconvolution,[Volterra discretization with L-curve criterion](../src/original/SR_TBG_BNIPhoenix_USA/AIFDeconvolution/AIF_deconvolution.py),,SR_TBG_BNI_PhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",AIFdeconvolution,,JA,completed +DCE/DSC,Miscellaneous,[calculate SNR](../src/original/DS_BW_VanderBiltUMC_USA/dcemri.py),,DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA",signal_to_noise_ratio,,tbd, +DCE/DSC,Miscellaneous,[calculate enhancement ratio](../src/original/DS_BW_VanderBiltUMC_USA/dcemri.py),,DS_BW_VanderBiltUMC_USA,"David Smith, Brian Welch","VanderBilt University Medical Center, USA",signal_enhancement_ratio,,tbd, +DSC,Input Functions,[automatic AIF selection](../src/original/JBJA_GUSahlgrenska_SWE/AIF_selection_auto/AIF_selection_automatic.py),"fully automatic, semi-automatic",JBJA_GUSahlgrenskaSWE,"Jesper Browall, Jonathan Arvidsson","Sahlgrenska University Hospital and Gothenburg University, Gothenburg, Sweden",AIF_selection_automatic.py,DOI: 10.1002/mrm.20759,tbd, +DSC,Leakage correction,[BSW](../src/original/SR_TBG_BNIPhoenix_USA/LeakageCorrection/bsw_leakagecorr.py),,SR_TBG_BNI_PhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",BSWleakagecorr,,SR,in-progress +DSC,Parameter derivation,"[CBV,CBF,MTT](../src/original/SR_TBG_BNIPhoenix_USA/DSCparameters/DSC_parameters.py)",,SR_TBG_BNI_PhoenixUSA,"Sudarshan Ragunathan, Laura Bell","Barrow Neurological Institute, USA",DSCparameters,,tbd, +DSC,Signal to deltaR2*,[single echo](../src/original/LCB_BNI_USA/dsc.py),,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA",,estimate_delta_R2s,tbd, +DSC,Signal to deltaR2*,[dual echo](../src/original/LCB_BNI_USA/dsc.py),,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA",,"estimate_delta_R2s, estimate_delta_R2s_dual_echo",tbd, +DSC,Signal to R2*,[dual echo](../src/original/LCB_BNI_USA/dsc.py),,LCB_BNI_USA,Laura Bell,"Barrow Neurological Institute, USA",,estimate_R2s,tbd, \ No newline at end of file diff --git a/doc/code_contributions_record.md b/doc/code_contributions_record.md new file mode 100644 index 00000000..bc82170e --- /dev/null +++ b/doc/code_contributions_record.md @@ -0,0 +1,89 @@ +| Technique | Category | Subcategory (link) | Notes | Subfolder | Authors | Institution | function/module name | doi | Tester | Test status (empty/in-progress/complete) | +|:------------|:------------------------|:---------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------------|:------------------------|:--------------------------------------|:---------------------------------------------------------------------------------------|:----------------------------------------------|:--------------------------------------------------------------------------------------|:---------|:-------------------------------------------| +| DCE | Bolus arrival time | [piecewise linear quadratic function](../src/original/LEK_UoEdinburgh_UK/PharmacokineticModelling/BAT_estimation.py) | Cheong et al (DOI: 10.1088/0031-9155/48/5/403) | LEK_UoEdinburgh | Lucy Kershaw | University of Edinburgh, UK | BAT_linquad | nan | tbd | nan | +| DCE | Bolus arrival time | fitting Kety (Tofts) model to first third of the curve | nan | LEK_UoEdinburgh | Lucy Kershaw | University of Edinburgh, UK | BAT_kety | nan | tbd | nan | +| DCE | Input Functions | load AIF | load from txt | MB_QBI_UoManchester_UK | Michael Berks | University of Manchester, UK | read_AIF | https://doi.org/10.21105/joss.03523 | tbd | nan | +| DCE | Input Functions | Parker AIF | nan | MB_QBI_UoManchester_UK | Michael Berks | University of Manchester, UK | compute_population_AIF | https://doi.org/10.21105/joss.03523 | JK/PvH | completed | +| DCE | Input Functions | patient-specific AIF | constructed from time-concentration data | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | patientSpecific | nan | tbd | nan | +| DCE | Input Functions | Parker AIF | Parker AIF, Parker-like AIF | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | Parker | nan | JK/PvH | completed | +| DCE | Input Functions | Manning AIF | Manning et al (https://doi.org/10.1002/mrm.28833) | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | ManningFast, ManningSlow | nan | tbd | completed | +| DCE | Input Functions | Heye AIF | Heye et al (https://doi.org/10.1016/j.neuroimage.2015.10.018) | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | Heye | nan | tbd | completed | +| DCE | Input Functions | AIF parameterization | nan | OG_MO_AUMC_ICR_RMH | Oliver Gurney-Champion, Matthew Orton | Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK | Cosine4AIF, Cosine8AIF | https://doi.org/10.1088/0031-9155/53/5/005; https://doi.org/10.1007/s00330-015-4012-9 | tbd | nan | +| DCE | Input Functions | Head-and-neck population AIF | Wong et al (DOI: https://doi.org/10.2967/jnumed.116.174433) | OG_MO_AUMC_ICR_RMH | Oliver Gurney-Champion, Matthew Orton | Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK | aifPopHN | nan | tbd | nan | +| DCE | Input Functions | Parker AIF | nan | OG_MO_AUMC_ICR_RMH | Oliver Gurney-Champion, Matthew Orton | Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK | aifPopPMB | nan | tbd | nan | +| DCE | Input Functions | load AIF | from txt | OGJ_OsloU_NOR | Ole Gunnar Johansen | University of Oslo, Norway | loadStandard | nan | tbd | nan | +| DCE | Input Functions | AIF parameterization | fit gamma-variate function | OGJ_OsloU_NOR | Ole Gunnar Johansen | University of Oslo, Norway | gammaVariateFit | nan | tbd | nan | +| DCE | Input Functions | Georgiou AIF | Georgiou et al (DOI: 10.1002/mrm.27524) | PvH_NKI | Petra van Houdt | the Netherlands Cancer Institute, the Netherlands | GeorgiouAIF | nan | JK/PvH | completed | +| DCE | Input Functions | Parker AIF | nan | PvH_NKI | Petra van Houdt | the Netherlands Cancer Institute, the Netherlands | ParkerAIF | nan | JK/PvH | completed | +| DCE | Input Functions | Parker AIF | nan | ST_USydAUS_DCE | Sirisha Tadimalla | University of Sydney, Australia | AIF, variableAIF | nan | JK/PvH | completed | +| DCE | Input Functions | preclinical AIF | McGrath et al (DOI: 10.1002/mrm.21959) | ST_USydAUS_DCE | Sirisha Tadimalla | University of Sydney, Australia | preclinicalAIF | nan | JK/PvH | completed | +| DCE | Miscellaneous | enhancement detection | check for enhancement | OG_MO_AUMC_ICR_RMH | Oliver Gurney-Champion, Matthew Orton | Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK | enhance | nan | tbd | nan | +| DCE | Parameter derivation | iAUC | nan | MB_QBI_UoManchester_UK | Michael Berks | University of Manchester, UK | compute_IAUC | https://doi.org/10.21105/joss.03523 | tbd | nan | +| DCE | Pharmacokinetic models | Tofts | NLLS fitting (+forward model) | DS_BW_VanderBiltUMC_USA | David Smith, Brian Welch | VanderBilt University Medical Center, USA | tofts_integral, fit_tofts_model | nan | tdd | nan | +| DCE | Pharmacokinetic models | extended Tofts | NLLS fitting (+forward model) | DS_BW_VanderBiltUMC_USA | David Smith, Brian Welch | VanderBilt University Medical Center, USA | ext_tofts_integral, fit_tofts_model | nan | tbd | nan | +| DCE | Pharmacokinetic models | Tofts | NLLS fitting (+ forward model) | LCB_BNI_USA | Laura Bell | Barrow Neurological Institute, USA | tofts_model, fit_tofts | nan | ST/OGC | completed | +| DCE | Pharmacokinetic models | 2-cmp exchange | forward model | LEK_UoEdinburgh | Lucy Kershaw | University of Edinburgh, UK | TwoCXM | nan | MJT | completed | +| DCE | Pharmacokinetic models | 2-cmp uptake | forward model | LEK_UoEdinburgh | Lucy Kershaw | University of Edinburgh, UK | TwoCUM | nan | MJT | completed | +| DCE | Pharmacokinetic models | AATH | forward model | LEK_UoEdinburgh | Lucy Kershaw | University of Edinburgh, UK | AATH | nan | tbd | nan | +| DCE | Pharmacokinetic models | extended Tofts | forward model | LEK_UoEdinburgh | Lucy Kershaw | University of Edinburgh, UK | ExtKety | nan | ST/OGC | completed | +| DCE | Pharmacokinetic models | Patlak | forward model | LEK_UoEdinburgh | Lucy Kershaw | University of Edinburgh, UK | Patlak | nan | MJT | completed | +| DCE | Pharmacokinetic models | Tofts | forward model | LEK_UoEdinburgh | Lucy Kershaw | University of Edinburgh, UK | Kety | nan | ST/OGC | completed | +| DCE | Pharmacokinetic models | 2-cmp exchange | LLSQ fitting (+forward model) | MB_QBI_UoManchester_UK | Michael Berks | University of Manchester, UK | two_cxm_model | https://doi.org/10.21105/joss.03523 | MJT | completed | +| DCE | Pharmacokinetic models | 2-cmp filtration | LLSQ fitting (+forward model) | MB_QBI_UoManchester_UK | Michael Berks | University of Manchester, UK | two_cfm_model | https://doi.org/10.21105/joss.03523 | tbd | nan | +| DCE | Pharmacokinetic models | active uptake and efflux (AUEM) | LLSQ fitting (+forward model) | MB_QBI_UoManchester_UK | Michael Berks | University of Manchester, UK | active_uptake_model | https://doi.org/10.21105/joss.03523 | tbd | nan | +| DCE | Pharmacokinetic models | dual-inlet general model | LLSQ fitting (+forward model) | MB_QBI_UoManchester_UK | Michael Berks | University of Manchester, UK | dibem | https://doi.org/10.21105/joss.03523 | tbd | nan | +| DCE | Pharmacokinetic models | extended Tofts | LLSQ fitting (+forward model) | MB_QBI_UoManchester_UK | Michael Berks | University of Manchester, UK | tofts_model | https://doi.org/10.21105/joss.03523 | ST/OGC | completed | +| DCE | Pharmacokinetic models | 2-cmp exchange | NLLS fitting to concentration values (incl forward model) | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | TCXM, EnhToPKP, ConcToPKP | nan | MJT | completed | +| DCE | Pharmacokinetic models | 2-cmp exchange | NLLS fitting to signal incl. water exchange (incl forward model) | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | TCXM, EnhToPKP, ConcToPKP | nan | MJT | completed | +| DCE | Pharmacokinetic models | 2-cmp uptake | NLLS fitting to concentration values (incl forward model) | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | TCUM, EnhToPKP, ConcToPKP | nan | MJT | completed | +| DCE | Pharmacokinetic models | 2-cmp uptake | NLLS fitting to signal incl. water exchange (incl forward model) | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | TCUM, EnhToPKP, ConcToPKP | nan | MJT | completed | +| DCE | Pharmacokinetic models | extended Tofts | NLLS fitting to concentration values (incl forward model) | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | ExtendedTofts, EnhToPKP, ConcToPKP | nan | ST/OGC | completed | +| DCE | Pharmacokinetic models | extended Tofts | NLLS fitting to signal incl. water exchange (incl forward model) | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | ExtendedTofts, EnhToPKP, ConcToPKP | nan | ST/OGC | completed | +| DCE | Pharmacokinetic models | Patlak | NLLS fitting to concentration values (incl forward model) | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | Patlak, EnhToPKP, ConcToPKP | nan | MJT | completed | +| DCE | Pharmacokinetic models | Patlak | NLLS fitting to signal incl. water exchange (incl forward model) | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | Patlak, EnhToPKP, ConcToPKP | nan | MJT | completed | +| DCE | Pharmacokinetic models | Patlak | LLSQ fitting | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | PatlakLinear | nan | MJT | completed | +| DCE | Pharmacokinetic models | steady-state vp | NLLS fitting to concentration values (incl forward model) | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | SteadyStateVp, EnhToPKP, ConcToPKP | nan | tbd | nan | +| DCE | Pharmacokinetic models | steady-state vp | NLLS fitting to signal incl. water exchange (incl forward model) | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | SteadyStateVp, EnhToPKP, ConcToPKP | nan | tbd | nan | +| DCE | Pharmacokinetic models | Tofts | NLLS fitting to concentration values (incl forward model) | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | Tofts, EnhToPKP, ConcToPKP | nan | ST/OGC | completed | +| DCE | Pharmacokinetic models | Tofts | NLLS fitting to signal incl. water exchange (incl forward model) | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | Tofts,EnhToPKP, ConcToPKP | nan | ST/OGC | completed | +| DCE | Pharmacokinetic models | extended Tofts | NLLS fitting (+forward model) | OG_MO_AUMC_ICR_RMH | Oliver Gurney-Champion, Matthew Orton | Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK | fit_tofts_model | nan | ST/OGC | completed | +| DCE | Pharmacokinetic models | 2-cmp exchange | LLSQ fitting (+ forward model) | OGJ_OsloU_NOR | Ole Gunnar Johansen | University of Oslo, Norway | twoCXM, fitToModelLLSQ | nan | MJT | completed | +| DCE | Pharmacokinetic models | extended Tofts | NLLS fitting (+ forward model) | OGJ_OsloU_NOR | Ole Gunnar Johansen | University of Oslo, Norway | ETM, fitToModelNLLS, fitToModelNLLS_parallel | nan | ST/OGC | completed | +| DCE | Pharmacokinetic models | extended Tofts | LLSQ fitting (+ forward model) | OGJ_OsloU_NOR | Ole Gunnar Johansen | University of Oslo, Norway | ETM, fitToModelLLSQ | nan | ST/OGC | completed | +| DCE | Pharmacokinetic models | Tofts | NLLS fitting (+ forward model) | OGJ_OsloU_NOR | Ole Gunnar Johansen | University of Oslo, Norway | TM, fitToModelNLLS, fitToModelNLLS_parallel | nan | ST/OGC | completed | +| DCE | Pharmacokinetic models | Tofts | LLSQ fitting (+ forward model) | OGJ_OsloU_NOR | Ole Gunnar Johansen | University of Oslo, NOR | TM, fitToModelLLSQ | nan | ST/OGC | completed | +| DCE | Pharmacokinetic models | 1-cmp | forward model | ST_USydAUS_DCE | Sirisha Tadimalla | University of Sydney, Australia | OneCompartment | nan | tbd | nan | +| DCE | Pharmacokinetic models | dual-inlet 1-cmp | forward model | ST_USydAUS_DCE | Sirisha Tadimalla | University of Sydney, Australia | DualInletOneCompartment | nan | tbd | nan | +| DCE | Pharmacokinetic models | dual-inlet ext Tofts | forward model | ST_USydAUS_DCE | Sirisha Tadimalla | University of Sydney, Australia | DualInletExtendedTofts | nan | tbd | nan | +| DCE | Pharmacokinetic models | dual-inlet high-flow 2-cmp Gadoxetate | forward model | ST_USydAUS_DCE | Sirisha Tadimalla | University of Sydney, Australia | DualInletconc_HF2CGM | nan | tbd | nan | +| DCE | Pharmacokinetic models | extended Tofts | forward model | ST_USydAUS_DCE | Sirisha Tadimalla | University of Sydney, Australia | ExtendedTofts | nan | ST/OGC | completed | +| DCE | Pharmacokinetic models | Tofts | forward model | ST_USydAUS_DCE | Sirisha Tadimalla | University of Sydney, Australia | Tofts | nan | ST/OGC | completed | +| DCE | Pharmacokinetic models | high flow 2-cmp Gadoxetate | forward model | ST_USydAUS_DCE | Sirisha Tadimalla | University of Sydney, Australia | nan | nan | tbd | nan | +| DCE | Pharmacokinetic models | Patlak | forward model | ST_USydAUS_DCE | Sirisha Tadimalla | University of Sydney, Australia | PatlakModel | nan | MJT | completed | +| DCE | Signal to Concentration | SPGR | two-steps: S->R1, R1->C | DS_BW_VanderBiltUMC_USA | David Smith, Brian Welch | VanderBilt University Medical Center, USA | r1eff_to_conc, dce_to_r1eff | nan | tbd | nan | +| DCE | Signal to Concentration | SPGR or GE-EPI | nan | LCB_BNI_USA | Laura Bell | Barrow Neurological Institute, USA | signal_to_conc, estimate_delta_R1 | nan | LK | completed | +| DCE | Signal to concentration | SPGR | reverse C->S also available | LEK_UoEdinburgh | Lucy Kershaw | University of Edinburgh, UK | SI2Conc | nan | LK | completed | +| DCE | Signal to concentration | SPGR | reverse C->S also available | MB_QBI_UoManchester_UK | Michael Berks | University of Manchester, UK | signal_to_concentration | https://doi.org/10.21105/joss.03523 | LK | completed | +| DCE | Signal to concentration | SPGR | two steps: S-> enhancement, enhancement -> C; reverse C->S also available | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | sign_to_enh, enh_to_conc | nan | LK | completed | +| DCE | Signal to concentration | SPGR | two steps: S->R1, R1 -> C; reverse C->S also available | OG_MO_AUMC_ICR_RMH | Oliver Gurney-Champion, Matthew Orton | Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK | dce_to_r1eff, r1eff_to_conc | nan | LK | completed | +| DCE | Signal to concentration | SPGR | reverse R1->C also available | ST_USydAUS_DCE | Sirisha Tadimalla | University of Sydney, Australia | signals2conc | nan | LK | completed | +| DCE | T1 | VFA | nonlinear | DS_BW_VanderBiltUMC_USA | David Smith, Brian Welch | VanderBilt University Medical Center, USA | fit_R1 | nan | tbd | nan | +| DCE | T1 | VFA | despot | McGill_VFA | Zaki Ahmed | McGill University, Canada | despot | nan | MJT | completed | +| DCE | T1 | VFA | novifast | McGill_VFA | Zaki Ahmed | McGill University, Canada | novifast | nan | MJT | completed | +| DCE | T1 | DESPOT1-HIFI | Fit any combination of (IR-)SPGR scans to estimate T1 | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | HIFI | nan | MJT | in-progress | +| DCE | T1 | VFA | linear | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | VFALinear | nan | MJT | complete | +| DCE | T1 | VFA | nonlinear | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | VFANonlinear | nan | MJT | complete | +| DCE | T1 | VFA | two flip angles | MJT_UoEdinburgh_UK | Michael Thrippleton | University of Edinburgh, UK | VFA2Points | nan | tbd | nan | +| DCE | T1 | VFA | two flip angles (linear) | OG_MO_AUMC_ICR_RMH | Oliver Gurney-Champion, Matthew Orton | Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK | R1_two_fas | nan | MJT | competed | +| DCE | T1 | VFA | nonlinear | OG_MO_AUMC_ICR_RMH | Oliver Gurney-Champion, Matthew Orton | Amsterdam University Medical Center, the Netherlands, Institute of Cancer Research, UK | R1_VFA | nan | MJT | competed | +| DCE | T1 | VFA | linear | ST_Sydney_AUS_T1 | Sirisha Tadimalla | University of Sydney, Australia | VFAT1mapping | nan | MJT | completed | +| DCE | T1 | VFA | nonlinear | ST_Sydney_AUS_T1 | Sirisha Tadimalla | University of Sydney, Australia | VFAT1mapping | nan | MJT | completed | +| DCE/DSC | AIF deconvolution | nan | nan | SR_TBG_BNI_PhoenixUSA | Sudarshan Ragunathan, Laura Bell | Barrow Neurological Institute, USA | AIFdeconvolution | nan | JA | completed | +| DCE/DSC | Miscellaneous | calculate SNR | nan | DS_BW_VanderBiltUMC_USA | David Smith, Brian Welch | VanderBilt University Medical Center, USA | signal_to_noise_ratio | nan | tbd | nan | +| DCE/DSC | Miscellaneous | calculate enhancement ratio | nan | DS_BW_VanderBiltUMC_USA | David Smith, Brian Welch | VanderBilt University Medical Center, USA | signal_enhancement_ratio | nan | tbd | nan | +| DSC | Input Functions | automatic AIF selection | fully automatic, semi-automatic | JBJA_GUSahlgrenskaSWE | Jesper Browall, Jonathan Arvidsson | Sahlgrenska University Hospital and Gothenburg University, Gothenburg, Sweden | AIF_selection_automatic.py | DOI: 10.1002/mrm.20759 | tbd | nan | +| DSC | Leakage correction | BSW | nan | SR_TBG_BNI_PhoenixUSA | Sudarshan Ragunathan, Laura Bell | Barrow Neurological Institute, USA | BSWleakagecorr | nan | SR | in-progress | +| DSC | Parameter derivation | CBV,CBF,MTT | nan | SR_TBG_BNI_PhoenixUSA | Sudarshan Ragunathan, Laura Bell | Barrow Neurological Institute, USA | DSCparameters | nan | tbd | nan | +| DSC | Signal to deltaR2* | single echo | nan | LCB_BNI_USA | Laura Bell | Barrow Neurological Institute, USA | nan | estimate_delta_R2s | tbd | nan | +| DSC | Signal to deltaR2* | dual echo | nan | LCB_BNI_USA | Laura Bell | Barrow Neurological Institute, USA | nan | estimate_delta_R2s, estimate_delta_R2s_dual_echo | tbd | nan | +| DSC | Signal to R2* | dual echo | nan | LCB_BNI_USA | Laura Bell | Barrow Neurological Institute, USA | nan | estimate_R2s | tbd | nan | \ No newline at end of file diff --git a/doc/convert_to_md.py b/doc/convert_to_md.py new file mode 100644 index 00000000..93d53261 --- /dev/null +++ b/doc/convert_to_md.py @@ -0,0 +1,5 @@ +import pandas as pd + +df = pd.read_csv('doc/code_contributions_record.csv') +with open('doc/code_contributions_record.md', 'w') as md: + df.to_markdown(buf=md, index=False) \ No newline at end of file